chr22-34409819-G-A

Position:

• chr22-34409819-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.912 in 151,710 control chromosomes in the GnomAD database, including 63,162 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.91 (63162 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0590

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.912 AC: 138292 AN: 151614 Hom.: 63113 Cov.: 31

Gnomad AFR AF: 0.925

Gnomad AMI AF: 0.947

Gnomad AMR AF: 0.936

Gnomad ASJ AF: 0.921

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.976

Gnomad FIN AF: 0.919

Gnomad MID AF: 0.924

Gnomad NFE AF: 0.886

Gnomad OTH AF: 0.902

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.912 AC: 138389 AN: 151710 Hom.: 63162 Cov.: 31 AF XY: 0.917 AC XY: 67924 AN XY: 74104

Gnomad4 AFR AF: 0.925

Gnomad4 AMR AF: 0.936

Gnomad4 ASJ AF: 0.921

Gnomad4 EAS AF: 1.00

Gnomad4 SAS AF: 0.976

Gnomad4 FIN AF: 0.919

Gnomad4 NFE AF: 0.886

Gnomad4 OTH AF: 0.903

Alfa AF: 0.904 Hom.: 8003

Bravo AF: 0.913

Asia WGS AF: 0.976 AC: 3374 AN: 3458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.57
DANN	Benign	0.58

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs169482; hg19: chr22-34805809;